Answer

For some reason, an old build has been removed from the combined update site, but the p2 metadata has not been refreshed. Or, the jar has been deleted but a reference to it remains in the category.xml files from which the site.xml is aggregated. In either case, you need to:

ssh build.eclipse.org

If you're unsure what you're about to do, back up the update site first before working on it.

If building locally on build.eclipse.org, changes should be more or less immediate.
If building remotely (eg., accessing the metadata via http://download.eclipse.org or from a mirror), wait at least 30-60 mins for replication to complete.

Finally, and this is very important, make sure you fix permissions on the newly created/edited files and folders, eg:

If you get permission denied errors, that's OK, as long as the files in the dir are all set to the correct group and are group-writeable (eg., -rw-rw-r-- or drwxrwxr-x)

Still a problem?

You may discover that some feature which on the update site includes the missing feature. So, when the p2 metadata is generated, p2 will scrape the list of features from the site.xml, then check each one's feature.xml for contained feature references. In the example above, Transaction's org.eclipse.emf.emfqtv.all.sdk_1.2.3.v200810041753-3539-FFBRDMVOp5jnPbgRbDUVz0G.jar feature references the missing validation feature jar thus:

If you intend to build from HEAD and have already enabled forceContextQualifier in your buildAll.xml, it looks like the problem is that only ONE feature jar was added. Checking the site.xml, we see that in fact only the examples feature was added.